Bioinformatics

by Edwards, David; Stajich, Jason; Hansen, David

• ISBN13: 9780387927374
• ISBN10: 0387927379
• Format: Hardcover
• Copyright: 2009-09-08
• Publisher: Springer Nature

Summary

Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory.The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

Author Biography

Janson Stajich earned a Bachelor of Science in Computer Science from Duke University in Durham, NC in 1999 and worked a programmer for the Center for Human Genetics at Duke University Medical Center for two years assisting in building systems supporting human disease gene mapping research. He completed a PhD in Genetics and Genomics from Duke University in 2006 followed by postdoctoral training at the University of California, Berkeley on fellowship from the Miller Institute for Basic Research in Science, Jason in currently an Assistant Professor of Bioinformatics in the Department of Plant Pathology and Microbiology at the University of California, Riverside. Jason's research focuses on the evolution of fungi studying change at gene and genome scale among populations and across the kingdom employing computational and comparative approaches. He is interested in the emergence and evolution of pathogens and the evolution of development and forms in multicellular fungi.

Table of Contents

DNA Sequence Databases	p. 1
Sequence Comparison Tools	p. 13
Genome Browsers	p. 39
Predicting Non-coding RNA Transcripts	p. 65
Gene Prediction Methods	p. 99
Gene Annotation Methods	p. 121
Regulatory Motif Analysis	p. 137
Molecular Marker Discovery and Genetic Map Visualisation	p. 165
Sequence Based Gene Expression Analysis	p. 191
Protein Sequence Databases	p. 209
Protein Structure Prediction	p. 225
Classification of Information About Proteins	p. 243
High-Throughput Plant Phenotyping - Data Acquisition, Transformation, and Analysis	p. 259
Phenome Analysis of Microorganisms	p. 279
Standards for Functional Genomics	p. 293
Literature Databases	p. 331
Advanced Literature-Mining Tools	p. 347
Data and Databases	p. 381
Programming Languages	p. 403
Index	p. 441
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